I agree with your line of thinking. In Gothic II, you were able to learn ways to take trophies- such as pelts, claws, horns, teeth, scales, etc.- and sell them or mount some of them. However, you had to learn the specific skill in order to harvest that particular trophy from the prey. It was a really cool feature that could be handled with the perk system, I think.
Love this idea. If Hunting was a skill (with Oblivion "perk mechanics" and survival mechanics), I would do it like this:
Hunting: Skill governs the price you get for the fallen prey and as a price modifier to the parts you obtain from the level perks, as well as a meat quality when you need to prepare a meal from your prey (depending also on a cooking skill). The perks would be:
25 - Apprentice : Acquire Pelts, Skins, Scales.
50 - Journeyman : Acquire Claws, Teeth, Horns.
75 - Expert : Acquire Items of magical properties if present (like a unicorn horn).
100 - Master : Your able to stuff your prey and sell it as a trophy at great prices.
Means that animals are no longer a source of alchemy ingredients until you are expert in hunting. I prefer the term Herb Lore over Alchemy anyways since we're never dealing with metals.
Prices. You either sell your prey for 1-5gp or cook it for nutrition. At Apprentice, you're able to kill with better precision increasing price of prey to 3-8gp. At Master, there is no blood spoilage anywhere and price goes up to 20-30. However, at Apprentice you also get to acquire additional stuff which you can sell, i.e. a Pelt. At Master, your skinning technique is well improved and increases the value of the Pelt. This goes for the rest too. So a Master Hunter would be able to obtain 100-300gp selling parts, or 250-350 selling the full trophy but there is the risk you fumble the process and ruins everything
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Myself, I'm a Master Fumbler
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Oh, and there is no freebies. Fell a dear and carry it, no big deal. Fell a Minotaur however, and you'll need a cart to drag it around. Never liked the Simon the Sorceror approach to encumbrance and how much you can fit into your magic hat.
The items you get can be further increased in value with Crafting skill. Turn pelts into clothes or rugs, or convert teeth to jewelery. I would love being able to craft my own neckless showing off to the world how many ogres I've killed